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At least 343 records · Page 19Linked to original sources

AI-integrated digital breeding for crop improvement.

Crop breeding increasingly depends on the effective integration and interpretation of large, heterogeneous datasets spanning genomic, phenotypic, multi-omics, and environmental layers. Conventional breeding approaches are often insufficient to capture the complex relationships among these data or to support timely selection decisions. Digital breeding can help address this limitation by complementing field experimentation, mixed models, and genomic prediction with the integration of biological data and computational prediction throughout the breeding process. In particular, the rapid advancement of artificial intelligence (AI) has improved the analysis of high-dimensional datasets and broadened its application to trait prediction, selection, and breeding design. Here, we review recent developments in AI-enabled digital breeding, encompassing genomic, phenomic, and multi-omics data generation and analysis, predictive modeling, explainable and generative AI, and data-driven breeding decision support. We further discuss emerging AI applications, their current contributions to crop research and breeding, and the major considerations affecting their reliable and practical implementation. Collectively, this review provides a structured understanding of the roles of AI across the digital breeding process and offers guidance for future methodological development and practical application in crop improvement.

artificial intelligence↗

Analysis of relationships between German heavy horse breeds based on pedigree information.

We analysed the relationship coefficients (R) between the four German heavy horse breeds South German Coldblood, Rhenish German Draught Horse, Schleswig Draught Horse and Black Forest Draught Horse. The relationship coefficient makes it possible to ascertain crossbreeding between the breeds over time, or autonomous developments of the breeds, respectively. The investigation revealed that the relationship coefficients between the German draught horse breeds were very low. The mean relationship coefficients between the four German heavy horse breeds were largest between the South German Coldblood and Schleswig Draught Horse (0.103%), whereas mean relationship coefficients were lowest between the Rhenish German and Black Forest Draught Horse (0.001%). The Rhenish German Draught Horse showed largest relationship coefficients with the Schleswig Draught Horse (0.09%), while the Black Forest Draught Horse was mostly related to the South German Coldblood (0.06%). The results reveal the presence of very few common progenitors of the breeds. The gene flow between the breeds is primarily due to crossbreeding of stallions and, especially, in the Rhenish German Draught Horse population breeding with a few mares from other German draught horse breeds.

Animals↗

[Genetic differentiation of domestic goose breeds in China].

The 1 042 bp control region of mitochondrial DNA from 84 geese of 15 domestic goose breeds was sequenced and genetic differentiation was analysed. Results showed that the interpopulation nucleotide divergence was highest (3.805% -4.067%) between Yili and the other 14 breeds. The average nucleotide diversity variation within different domestic breeds was 0 - 0.116%. Excluding the Yili, the interpopulation nucleotide divergence between Huoyan and the remaining breeds, was 0.211% - 0.272%, which was significantly higher than that between any other two breeds (0 -0.094%). During the formation of domestic breeds in China,there is an association between the genetic differentiation of domestic geese and their geographic distribution. The divergence time of Huoyan breed was relatively earlier and genetic drift may have been the main factor to affect the genetic differentiation of the Huoyan breed (Nm = 0.02 -0.54). On the other hand, gene flow is the main reason for the lack of a clear differentiation among the remaining 13 Chinese domestic geese breeds (Nm = 12.0 - 65.33).

Animals↗

[Genetic diversity of seven miniature pig breeds (strains) analyzed by using microsatellite markers].

Twenty-seven microsatellite markers recommended by the Food and Agriculture Organization (FAO) and the International Society for Animal Genetics (ISAG) were used to analyze the genetic diversities of 7 Chinese native miniature pig breeds/strains (Jiuyang Xiang Pig, Jianbai Xiang Pig, Congjiang Xiang Pig, Huanjiang Xiang Pig, Black Xiang Pig, Wuzhishan Pig, and Diannan Small Ear Pig) and 3 western pig breeds (Duroc, Large White, and Landrace). The results indicate that there exists, in general, a high degree of genetic variability within the 7 miniature pig breeds. However, the genetic variability in Jiuyang Xiang Pig, Jianbai Xiang Pig, Huanjiang Xiang Pig, and Congjiang Xiang Pig (average PICs being 0.61-0.64) was significantly lower than that in the other three miniature pig breeds (average PICs being 0.60-0.84). The genetic divergence among Jiuyang, Jianbai, Huanjiang, and Congjiang was very small (Nei's standard genetic distances being 0.12-0.22), but it was large between them and the other three miniature pig breeds (Nei's standard genetic distances being 1.61-1.96), and even larger between them and the three foreign breeds (Nei's standard genetic distances being 1.99-3.30). Cluster analysis reveals three obvious clusters for the 10 breeds: Jiuyang, Jianbai, Huanjiang, and Congjiang are in one cluster, the other three miniature pig breeds in the other, and the three foreign breeds in the third. These results are consistent with the geography distribution and origin of these breeds.

Animals↗

Orientation behaviour of toads (Bufo bufo) displaced from the breeding site.

The sensory basis and spatial range of orientation to the breeding site were studied in the toad Bufo bufo, during two breeding seasons. Toads were displaced passively from their breeding pond and fitted with a tracking device to record the path of migration in individuals. The directional choice and the straightness of trails after release were used to quantify the effect of experimental treatments. In both years, control (untreated) toads headed to the breeding site with the same precision at all release sites. The initial orientation of toads blinded by opaque tape over their eyes did not differ from controls, but the return paths were not as direct. The directional choice of anosmic toads was apparently random, however, individuals followed a straight path in a chosen direction. Anosmic toads also blinded were completely disoriented, moving in cycloid trails. Bar magnets glued to the head caused an increase in dispersion of toads. However, in some individual releases a directional bias without increased dispersion was observed. Sky conditions (clear or overcast) did not influence the initial orientation or the dispersion of toads. Nevertheless, the breeding site component was significantly correlated with wind direction in relation to the breeding site. Wind blowing from the breeding site improved the initial orientation, whereas wind from the opposite direction reduced the breeding site component. The spatial range for the ability to relocate the breeding pond after displacement exceeded 3 km, but the time taken to select the correct direction increased with the displacement distance. The results indicate that after displacement the initial orientation of B. bufo is based mainly on olfactory and magnetic cues, with visual control of straightness.

Animals↗

The relationship between ram breeding capacity and flock fertility.

The effect of breeding capacity of rams on flock fertility was studied by exposing each of 15 rams to 1 of 15 flocks of 200 naturally-cycling ewes for 17 days. Five of the rams were arbitrarily designated as being of high breeding capacity (mean+/-SEM = 14.7+/-0.5 services in 2 3-hour pen breeding tests); five rams were designated as being of medium capacity (7.3 +/- 0.2); and the remaining five were designated as being of low breeding capacity (1.7 +/- 0.5). Breeding capacity was shown to be positively correlated with the number of services during flock mating, to the number of ewes mated and to insemination success. Breeding capacity as measured in a pen test of shorter duration (1 hour) was shown to be similarly related to flock fertility. Further, the number of services during flock mating was also positively correlated with the number of ewes mated and impregnated, as well as to the number of fetuses conceived and to insemination success. Breeding frequency of the ram is, therefore, closely related to flock fertility, but breeding capacity, as measured in the present study, is only a moderately accurate indicator of breeding frequency.

Journal Article↗

Hormonal relationships during the periovulatory period among ewe breeds known to differ in fertility after cervical artificial insemination with frozen thawed semen.

Our previous work indicates that ewe breed differences in fertility following cervical AI with frozen-thawed semen are due to failure of normal sperm transport and/or early embryo development. Here we examined differences in hormone concentrations about the time of ovulation among more (Finnish Landrace and Belclare) and less (Suffolk and Texel) fertile ewes after AI with frozen thawed semen. In Experiment 1, oestradiol concentrations were measured in samples collected frequently from 12h before to 18h after the LH surge and progesterone was measured in samples collected from 9 to 27h after the LH surge in Suffolk (n=24), Texel (n=20) and Finnish Landrace (n=27) ewes. In Experiment 2, oestradiol concentrations were measured in samples collected frequently from 24h before to 6h after the LH surge and progesterone was measured in samples collected from 6h to 6 days after the LH surge in Suffolk (n=35) and Belclare (n=30) ewes. In Experiment 1, there was an effect of breed, time and their interaction (P<0.001) on oestradiol concentrations between -12 and +6h but only breed differences at +12 and +18h (P<0.01). Progesterone concentrations increased over time (P<0.001) and the rate of increase was significantly greater in Finnish Landrace than in the other two breeds. In Experiment 2, oestradiol concentrations were unaffected by breed. There was an interaction between breed and time with the rate of increase of progesterone being greater in Belclare than Suffolk ewes (P<0.001). In conclusion, differences in hormone concentrations in the periovulatory period are not consistent with ewe breed differences in fertility; however, we have showed that progesterone concentrations rise earlier in the more prolific breeds and suggest that this may explain reported ewe breed differences in embryo development.

Animals↗

Growth and reproductive development from weaning through 20 months of age among breeds of bulls in subtropical Florida.

To determine the effect of breed on growth and reproductive development, weaned bulls in each of 2 yr were managed as a single group for approximately a year. In Year 1, the study group consisted of 24 Angus, 24 Brahman, 20 Hereford and 14 Senepol bulls, while in Year 2, it contained 25 Angus, 17 Brahman. 13 Romosinuano and 9 Nellore x Brahman bulls. Body and testicular growth measurements were recorded at 6-wk intervals. At approximately 1 yr of age and quarterly thereafter (4 periods), bulls were evaluated for libido, pubertal status, and GnRH-induced LH and testosterone secretion. Significant breed-by-age interactions occurred for most growth measurements. Brahman bulls (Bos indicus ) were (P < 0.05) older and heavier at puberty than Angus, Hereford, Senepol and Romosinuano bulls (Bos taurus ). Libido scores were lowest for Brahman and Nell ore x Brahman bulls (Bos indicus ). highest for Angus and Hereford bulls (temperate Bos taurus breeds) and intermediate for Senepol and Romosinuano bulls (tropical Bos taurus breeds; P < 0.05). Differences were not consistent among breeds or between years for GnRH-induced LH secretion. In both years, basal testosterone concentrations and areas under the GnRH-induced testosterone curve were higher (P < 0.05) for Angus and Hereford bulls (temperate breeds) than for Brahman, Senepol, Romosinuano and Nellore x Brahman bulls (tropical breeds). In conclusion, reproductive development of Senepol and Romosinuano bulls (tropical Bos taurus breeds) was more similar to Angus and Hereford bulls (temperate Bos taurus breeds) than to Brahman and Nellore x Brahman bulls (Bos indicus ).

Journal Article↗

Effects of point-source PCB contamination on breeding performance and post-fledging survival in the dipper Cinclus cinclus.

Despite widespread information on the incidence and biochemical effects of polychlorinated biphenyls (PCBs) in birds, field studies of effects on population processes are still scarce. This is particularly so in passerines. We therefore assessed breeding performance and post-fledging survival in dippers, Cinclus cinclus, breeding along the Afon Mule, a Welsh river where previous work indicated locally elevated PCB concentrations. We hypothesised that marked toxicological effects, including endocrine disruption, would be detectable as altered clutch-size, hatching success, nest success, brood-size, post-fledging survival or recruitment to the breeding population. Congener-specific analysis of PCBs in failed and deserted dipper eggs during 1990-93 revealed that geometric mean concentrations were four to 20 times higher along the Mule than elsewhere in Wales, UK. PCB signatures also varied highly significantly from other locations, with congeners 138, 153 and 180 dominant at the contaminated site, but 118 or 170 more frequent in eggs elsewhere. Subsequent analysis of surface runoff confirmed a small breaker's yard as a point source. Neither laying dates, clutch-sizes, brood-sizes, nest failure nor hatching failure along the contaminated Mule (n=46 breeding attempts and 218 eggs) differed significantly from dippers along adjacent reference rivers (n=82 breeding attempts and 315 eggs) or Welsh rivers as a whole (n=332 breeding attempts and 1534 eggs). Subsequent recaptures of breeding dippers ringed initially as nestlings were nearly identical between the Mule (7.7% of 182 nestlings), the reference set (7.5% of 323 nestlings) and all other Welsh rivers (7.3% of 2821 nestlings). These data illustrate the value of congener-specific analysis of bird's eggs in indicating local PCB sources. The data show also that PCBs can occur in dipper eggs at total concentrations of 0.49 (geometric mean)-1.29 (upper quartile) microg g(-1) wet mass without effects on breeding performance and survival. These values are below those at which biochemical or reproductive effects on other passerines have been detected, but above current concentrations in any other population of European dippers for which PCB data are available. Population effects by PCBs on European dippers are therefore unlikely. Survivors from locally contaminated sites like that in our study might allow field assessments of second-generation effects on breeding performance in wild birds that have developed under PCB exposure.

Journal Article↗

Evaluation of the genetic variability of 23 bovine microsatellite markers in four Belgian cattle breeds.

The polymorphism of 23 microsatellites in the four main cattle breeds in Belgium (Holstein Friesian, Belgian Blue, Belgian Red Pied and East Flemish) was analysed. Heterozygosity, polymorphism information content, the effective number of alleles, exclusion probability and the probability of genotypic identity for two random individuals were calculated for all microsatellites and all breeds. The Belgian Blue breed is generally a little less polymorphic in comparison with the other three breeds. Estimates of the genetic distances between these breeds confirmed the widely accepted proposition that the Belgian Blue is the most genetically distinct of these breeds. The three other breeds are likely to become one population, given current breeding strategies. Exclusion probabilities in parentage control cases are > 0.9999 in all four breeds when all 23 microsatellites are used and > 0.98 with only the two most polymorphic multiplexes.

Animals↗

Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers.

Genotype data from 20 microsatellites typed in 253 animals is used here to assess the genetic structure of seven European pedigree cattle breeds. Estimation of genetic subdivision using classical drift-based measures shows that the average proportion of genetic variation among breeds varies between 10 and 11% of the total, depending on the estimator used. We demonstrate that a simple allele-sharing genetic distance parameter can be used to construct a dendrogram of relationships among animals. This phylogenetic tree displays a remarkable degree of breed clustering and reflects an extensive underlying kinship structure, particularly for the Swiss Simmental breed and four breeds originating from the British Isles. Condensation of allele frequencies and individual genotypic compositions using principal component analysis is also used to investigate genetic structure among breeds and individual animals. In addition, the underlying genetic demarcation of European cattle breeds is emphasized in simulations of breeds assignment using allele frequency distributions from samples of microsatellite loci. Correct breed designation can be inferred with accuracies approaching 100% using data from a panel of 10 microsatellite loci.

Alleles↗

Temporal changes in genetic variation of north European cattle breeds.

Temporal changes in genetic variation within and between 13 North European cattle breeds were evaluated using erythrocyte antigen systems and transferrin protein as genetic markers. Current data on allele frequency distributions of markers in large commercial and smaller endangered native cattle breeds were compared to data published during 1956 to 1975. Intrabreed genetic variation was quantified by conventional parameters (e.g. heterozygosity, average number of alleles per locus) and migration by the effective migration rate. The neighbour-joining dendrogram of relationships between old and present cattle populations was constructed using Nei's standard genetic distance. Variance effective population size was estimated from changes in allele frequencies over time. Comparison of old and new data indicated some significant changes in allele frequencies. In six of the breeds, a few low-frequency alleles in the old data were absent in the present samples. Heterozygosity remained stable in most breeds. The harmonic means for variance effective population size ranged between 30 and 257. Current results indicate that despite marked declines in total population sizes, North European native cattle breeds have retained a reasonably high genetic diversity. However, their genes contribute less than previously to genetic variation of Nordic production breeds. Commercial breeds do not appear to have a larger effective population size than native breeds. The present effective population sizes imply that Nordic breeds could have lost from 1 to 11% of their heterozygosity over a 20-40-year period.

Animals↗

Indigenous domestic breeds as reservoirs of genetic diversity: the Argentinean Creole cattle.

Contrary to highly selected commercial breeds, indigenous domestic breeds are composed of semi-wild or feral populations subjected to reduced levels of artificial selection. As a consequence, many of these breeds have become locally adapted to a wide range of environments, showing high levels of phenotypic variability and increased fitness under natural conditions. Genetic analyses of three loci associated with milk production (alpha(S1)-casein, kappa-casein and prolactin) and the locus BoLA-DRB3 of the major histocompatibility complex indicated that the Argentinean Creole cattle (ACC), an indigenous breed from South America, maintains high levels of genetic diversity and population structure. In contrast to the commercial Holstein breed, the ACC showed considerable variation in heterozygosity (H(e)) and allelic diversity (A) across populations. As expected, bi-allelic markers showed extensive variation in He whereas the highly polymorphic BoLA-DRB3 showed substantial variation in A, with individual populations having 39-74% of the total number of alleles characterized for the breed. An analysis of molecular variance (AMOVA) of nine populations throughout the distribution range of the ACC revealed that 91.9-94.7% of the total observed variance was explained by differences within populations whereas 5.3-8.1% was the result of differences among populations. In addition, the ACC breed consistently showed higher levels of genetic differentiation among populations than Holstein. Results from this study emphasize the importance of population genetic structure within domestic breeds as an essential component of genetic diversity and suggest that indigenous breeds may be considered important reservoirs of genetic diversity for commercial domestic species.

Alleles↗

Plasma luteinizing hormone and testosterone concentrations in different breeds of young beef bulls in the tropics.

Plasma concentrations of luteinizing hormone (LH) and testosterone were measured at 3, 8, and 11 months of age in 48 Africander cross (AX), 24 Brahman cross (BX), 21 Hereford-Shorthorn, selected (HSS) and 14 Hereford-Shorthorn, random-bred (HSR) bulls. In all breeds plasma LH was lower (P less than 0.01) at 8 months (1.7 ng/ml) than at 3 months (2.6 ng/ml) or at 11 months (2.6 ng/ml). Over all ages there were no differences among breeds in mean plasma LH (AX 2.4, BX 2.4, HSS 1.8, HSR 2.2 ng/ml) and no breed X age interactions. In contrast, plasma testosterone increased significantly (P less than 0.01) with age at a faster rate in the AX breed, resulting in a significant (P less than 0.05) breed X age interaction. Testosterone concentrations, though similar among breeds at 3 months of age (0.45 ng/ml), were much higher (P less than 0.01) by 11 months in AX (2.56 ng/ml) than in BX (1.30 ng/ml), HSS (0.78 ng/ml) or HSR (0.66 ng/ml) bulls. Although LH did not differ among the breeds studied, the more pronounced increase in testosterone with age in the Africander cross bulls is consistent with the higher level of fertility commonly observed in this breed when compared to Brahman cross and Hereford-Shorthorn breeds during natural mating in Queensland.

Aging↗

Analysis of genetic variation in 28 dog breed populations with 100 microsatellite markers.

Dog breeds were created by man choosing for select phenotypic traits such as size, shape, coat color, conformation, and behavior. Rigorous phenotypic selection likely resulted in a loss of genetic information. The present study extends previous dog population observations by assessing the genotypic variation within and across 28 breeds representing the seven recognized breed groups of the American Kennel Club (AKC). One hundred autosomal microsatellite markers distributed across the canine genome were used to examine variation within breeds. Resulting breed-specific allele frequencies were then used in an attempt to elucidate phylogeny and genetic distances between breeds. While the set of autosomal microsatellites was useful in describing genetic variation within breeds, establishing the genetic relatedness between breeds was less conclusive. A more accurate determination of breed phylogeny will likely require the use of single-nucleotide polymorphisms (SNPs).

Animals↗

Chemical classification of cattle. 1. Breed groups.

From approximately 1000 papers with data on protein polymorphism in some 216 breeds of cattle, 10 polymorphic proteins were compared in means and variances of gene frequencies (arcsin p 1/2) for ten well-recognized breed groups for 196 of the breeds. The polymorphic proteins were alpha-lactalbumin, beta-lactoglobulin, caseins (alpha s1, beta and chi), serum albumin, transferrin, haemoglobin, amylase I and carbonic anhydrase II. The breed groups were North European, Pied Lowland, European Red brachyceros, Channel Island brachyceros, Upland brachyceros, primigenius-brachyceros mixed, primigenius, Indian Zebu, African Humped (with Zebu admixture), and African Humped (Sanga). The coherence within groups and the differences between groups are often impressive. Only carbonic anhydrase II fails to differentiate at least some of the major breed groups. In some cases paradoxical distributions of rare genetic variants can be explained by a more detailed inspection of breed history. The chemical data support the morphological and geographical divisions of cattle into major breed groups. There are three distinct but related brachyceros groups; for some polymorphisms the two Channel Island breeds, the Jersey and the Guernsey, are quite divergent. Although some authorities have considered the Pied Lowland as primigenius, it is a very distinct breed group.

Amylases↗

Analysis of genetic diversity and the determination of relationships among western Mediterranean horse breeds using microsatellite markers.

The distribution of genetic diversity and the genetic relationships among western Mediterranean horse breeds were investigated using microsatellite markers. The examined sample included seven Spanish and three Italian local horse breeds and populations, plus a Spanish Thoroughbred outgroup. The total number of animals examined was 682 (on average 62 animals per breed; range 20-122). The microsatellite marker set analysed provided 128 alleles (10.7 alleles per locus). Within-breed genetic diversity was always high (>0.70), with breeds contributing about 8% of the total genetic variability. The mean molecular coancestry of the entire population examined was 0.205, Losino being the breed that contributed most. In addition to Nei's standard and Reynolds' genetic distances, pair-wise kinship distance and molecular coancestry were estimated. Remarkably similar breed rankings were obtained with all methods. Clustering analysis provided an accurate representation of the current genetic relationships among the breeds. Determining coancestry is useful for analysing genetic diversity distribution between and within breeds and provides a good framework for jointly analysing molecular markers and pedigree information. An integrated analysis was undertaken to obtain information on the population dynamics in western Mediterranean native horse populations, and to better determine conservation priorities.

Alleles↗

Frequencies of PrP genotypes in 38 breeds of sheep sampled in the National Scrapie Plan for Great Britain.

Between October 2001 and January 2003 the prion protein (PrP) genotypes of over 250,000 sheep were determined through the operation of the National Scrapie Plan (NSP); the results for 38 breeds were analysed to provide an estimate of the underlying PrP genotype distribution of the British sheep population. Although there was marked variability among the genotype profiles of the different breeds, several trends emerged. A comparison of the allele frequencies demonstrated that the breeds could be grouped into three categories: breeds dominated by ARR and ARQ in which the frequency of ARR exceeded the frequency of ARQ; breeds dominated by ARR and ARQ in which the frequency of ARQ exceeded the frequency of ARR; and breeds with significant levels of either AHQ, ARH or VRQ. Hill breeds were more likely to have a lower proportion of animals at low risk of scrapie (NSP type 1) and a higher proportion of animals at an intermediate risk of scrapie (NSP type 3) than other breeds. Most breeds had a small proportion of animals at high risk of scrapie (NSP type 5). The frequency of ARR/VRQ (NSP type 4) was variable.

Animals↗